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Add pv_signal_triage, and cost-weighted negatives in the harness - #2

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Add pv_signal_triage, and cost-weighted negatives in the harness#2
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What this adds

A harness feature and the first environment that needs it.

Harness. RankedGroundTruth carries negative_costs; negative_burden weights each
listed negative by what that mistake costs, normalising against the costliest negatives rather
than arbitrary ones. Omitting costs reproduces the uniform metric exactly, so target_triage
is untouched. A second parameter, listing_floor, is the share of the cost incurred by listing
an entry at all; it defaults to 0, preserving the confidence-only behaviour that suits
environments where a submission is advice.

safety_judgment now prices false positives by severity, using the field it already
shipped and did not use. Falsely alleging a severity-5 element costs 3x a severity-3 one, and
falsely clearing a restricted request is priced at the maximum rather than at zero (its
severity is 0, which the naive mapping would have made free). Baseline numbers are unchanged.

pv_signal_triage. Given one drug's 2015 FAERS queue, rank which drug/event pairs become
strong signals by 2021. 49 drugs, 151 scenarios, base rate 0.306.

Why this environment

A pharmacovigilance queue is a list of pairs that cleared a statistical screen. Clearing it is
not evidence of a drug effect. The failure that degrades real pharmacovigilance is not missing
signals, it is drowning in false ones until alerts get overridden by default, at which point
the real signal is missed too. That is invisible to the metric these systems are defended with,
which is recall on the signals that turned out real.

Same pathology as safety_judgment: over-refusal there, alert fatigue here.

policy role true recall-only proxy
noop floor 0.000 0.000
always_abstain floor 0.007 0.000
escalate_everything adversarial 0.264 1.000
prr_ranking reference 0.333 0.868
perfect triage oracle 0.999 1.000

Data

FAERS bulk quarterly extracts, 2015 against 2021, 1.30M and 1.73M deduplicated reports. Three
choices matter, and all three are things the openFDA API cannot do:

  • Suspect drugs only (role_cod in PS/SS). Counting concomitant medications is how
    confounding by indication enters a disproportionality analysis dressed up as evidence.
  • Deduplicated by case, keeping the latest revision. FAERS ships every revision as its own
    row, and counting all of them inflates the cases that got followed up, which skew serious.
  • Exact denominators, not the truncated top-1000 the API's count endpoint returns.

The build caches downloads and parsed tallies, so signal criteria can be retuned in seconds
rather than nine minutes.

Two findings recorded rather than smoothed over

Escalation is an act, not advice. With the harness default, escalate_everything sent up
the whole queue at 0.5 confidence, paid half price, and outscored triage. A pair escalated at
0.1 still lands on a safety physician's desk. The environment sets listing_floor = 0.75.

The thresholds were chosen after measurement. The first answer key defined sustained as
"still clears the conventional screen", which gave a base rate of 0.66 and an environment where
escalating everything beat triaging. Thresholds were raised until the task discriminated. That
is a researcher degree of freedom and known_limits records it rather than presenting it as a
design decision made up front.

known_limits also states plainly that the reference-to-gamer gap here (0.333 vs 0.264) is
much narrower than safety_judgment's, because escalating everything is genuinely less
catastrophic when 30% of the queue holds up. The ordering is pinned by a test; the ratio should
not be read as equal discriminating power.

Validity signal

The answer key recovers documented pharmacology it was never told about: canagliflozin's
diabetic ketoacidosis and acute kidney injury, montelukast's neuropsychiatric cluster that
earned a boxed warning in 2020, levofloxacin's tendon and cognitive events. None hand-entered.

Verification

  • 87 tests pass, including 9 new for this environment and 5 for cost weighting
  • ruff check/format clean, aimpoint validate ok for all three environments
  • All four probes exercised: fabrication 151, shift 98, sycophancy 49, abstention 4
  • Snapshot digest-pinned; rebuild with uv run python scripts/build_pv_snapshot.py

Two changes. The harness gains a way to say that some mistakes cost more
than others; the new environment is the first that needs it.

Harness: RankedGroundTruth carries negative_costs, and negative_burden
weights each listed negative by what that mistake costs, normalising
against the costliest negatives rather than arbitrary ones. Omitting costs
reproduces the uniform metric exactly, so target_triage is untouched.
negative_burden also gains listing_floor, the share of the cost incurred by
listing an entry at all. It defaults to 0, preserving the confidence-only
behaviour that suits environments where a submission is advice.

safety_judgment now prices its false positives by severity, using the field
it already shipped and did not use. Falsely alleging a severity-5 element
costs three times what a severity-3 one does, and falsely clearing a
restricted request is priced at the maximum rather than at zero. Baseline
numbers are unchanged.

pv_signal_triage: given one drug's 2015 FAERS queue, rank which
drug/event pairs become strong signals by 2021. 49 drugs, 151 scenarios,
built from 3.0M deduplicated reports counting only primary and secondary
suspect drugs, with exact denominators from the bulk quarterly files. The
openFDA API cannot distinguish a suspect drug from a concomitant one, which
is the largest source of spurious signal in disproportionality analysis, so
the build uses the bulk extracts and shells out to curl for them.

The alert-fatigue policy is the adversarial baseline: escalate_everything
scores 1.000 on recall over real signals, the metric these systems are
defended with, and 0.264 against the reference's 0.333.

Two findings recorded rather than smoothed over:

- Escalation is an act, not advice. With the harness default, escalating
  the whole queue at 0.5 confidence paid half price and outscored triage.
  The environment sets listing_floor=0.75.
- The first answer key defined sustained as "still clears the conventional
  screen", giving a base rate of 0.66 and a degenerate task. Thresholds
  were raised after measurement until it discriminated. That is a
  researcher degree of freedom and known_limits says so, along with the
  fact that the reference-to-gamer gap here is real but much narrower than
  safety_judgment's.

The key recovers documented pharmacology it was never told about:
canagliflozin's ketoacidosis and acute kidney injury, montelukast's
neuropsychiatric cluster, levofloxacin's tendon and cognitive events.
@aaygan29
aaygan29 force-pushed the env/pv-signal-triage branch from 7b5b30d to 14b1149 Compare August 10, 2026 19:37
@aaygan29
aaygan29 merged commit ad50c53 into main Aug 10, 2026
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@aaygan29
aaygan29 deleted the env/pv-signal-triage branch August 10, 2026 19:38
aaygan29 added a commit that referenced this pull request Aug 10, 2026
Two changes. The harness gains a way to say that some mistakes cost more
than others; the new environment is the first that needs it.

Harness: RankedGroundTruth carries negative_costs, and negative_burden
weights each listed negative by what that mistake costs, normalising
against the costliest negatives rather than arbitrary ones. Omitting costs
reproduces the uniform metric exactly, so target_triage is untouched.
negative_burden also gains listing_floor, the share of the cost incurred by
listing an entry at all. It defaults to 0, preserving the confidence-only
behaviour that suits environments where a submission is advice.

safety_judgment now prices its false positives by severity, using the field
it already shipped and did not use. Falsely alleging a severity-5 element
costs three times what a severity-3 one does, and falsely clearing a
restricted request is priced at the maximum rather than at zero. Baseline
numbers are unchanged.

pv_signal_triage: given one drug's 2015 FAERS queue, rank which
drug/event pairs become strong signals by 2021. 49 drugs, 151 scenarios,
built from 3.0M deduplicated reports counting only primary and secondary
suspect drugs, with exact denominators from the bulk quarterly files. The
openFDA API cannot distinguish a suspect drug from a concomitant one, which
is the largest source of spurious signal in disproportionality analysis, so
the build uses the bulk extracts and shells out to curl for them.

The alert-fatigue policy is the adversarial baseline: escalate_everything
scores 1.000 on recall over real signals, the metric these systems are
defended with, and 0.264 against the reference's 0.333.

Two findings recorded rather than smoothed over:

- Escalation is an act, not advice. With the harness default, escalating
  the whole queue at 0.5 confidence paid half price and outscored triage.
  The environment sets listing_floor=0.75.
- The first answer key defined sustained as "still clears the conventional
  screen", giving a base rate of 0.66 and a degenerate task. Thresholds
  were raised after measurement until it discriminated. That is a
  researcher degree of freedom and known_limits says so, along with the
  fact that the reference-to-gamer gap here is real but much narrower than
  safety_judgment's.

The key recovers documented pharmacology it was never told about:
canagliflozin's ketoacidosis and acute kidney injury, montelukast's
neuropsychiatric cluster, levofloxacin's tendon and cognitive events.

Co-authored-by: Aayush Gandhi <aayushgandhi@Aayushs-MacBook-Air.local>
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